Enzymes

two great animations, used in class but worth another look for review...

This does an especially good job of illustrating allosteric enzymes and their regulation

Use this to convince yourself of the trends in graphs showing the effect on enzyme activity by (1) pH, (2) temperature and (3) substrate concentration. Also a great way to see the reasons behind the effect of inhibitors.

Here's a short treatment of the progression of scientific thought about how enzymes work...and the change form an earlier simpler model (Lock and Key) to a newer more complicated (Induced Fit) idea. (click image to increase size)

Lactose Tolerance - a preview of evolution and an application of biochemistry

3.4/7.2

Animation showing the detail of DNA replication

Another fine animation from Giannini at St. Olaf...Once you are comfortable with all the different "players" in this mechanism, label and color code the p99 7& p101 in Biozone workbook.

How do we know that DNA replication is semi-conservative?

Click on the pictures of Meselson and Stahl to see their experiments that verified this mechanism for DNA replication. Then try DBQ 2 below.

Here are three DBQ's from the Biology course Companion Book...complete them as though you were taking an exam...paying close attention to the command terms.

DBQ 1

DBQ 2

DBQ1 (answer)1. The sugars are different (ribose v. deoxyribose); RNA contains uracil while DNA contains thymine2. DNA is double stranded while RNA is single stranded3. DNA RNA Double stranded Single stranded Contains deoxyribose Contains ribose Contains thymine Contains uracil 4. Both are polymers of nucleotides/nucleic acids; They both have the bases adenine, cytosine and guanine; The sugar in both is a pentose; Both have a backbone of phosphate-sugar- phosphate.

DBQ2 (answer) ALSO SEE THE ANIMATION DIRECTLY ABOVE1. A DNA molecule composed of only N-14 should have a peak at 1.710. 2. After one generation grown in N-14, there was no peak at 1.710. 3. Therefore replication is not conservative. 4. If dispersive, no matter how many generations, all molecules would have same ratio of N-14 to N-15. 5. Not dispersive as there would always be only one peak and second generation grown in N-14 has two peaks.

DBQ3 (answer)1. More radioactive fragments of all sizes at 30 seconds; Increase in ratio of larger fragments to smaller fragments at 30 seconds/2 peaks at 30 seconds versus one peak at 10 seconds.2. Two peaks suggests two different sizes of molecules predominate; Higher peak represents large number of small
fragments/lagging strands;Smaller peak represents a number of longer
fragments/leading strands. 3. If lagging strands are joined together by DNA ligase, then the number of initial small molecules would decrease and the number of larger molecules would increase. This is what is observed so the hypothesis is supported.

Bio Song

Listen to my explanationBout to teach you replicationGet ready cause this is how it goes

First start with breaking the bondsThe base pairs should correspondThe helicase does split the strandsWhere it starts is the origin

Start the splitting by rich A TThat’s because only two bonds betweenCan’t start by C and GBonds between are more like three

Get ready for the important stepYou can already guess what’s nextThat’s right RNA Primase

They draw RNA nucleotidesWhich then bond to DNA sideThis is due to the hydrogen bondsIn which the base pairs should correspond

Listen to my explanationGonna give you a educationBetween me and you no stipulationPlease don’t hate cause that good sensationTryin’ to teach you replicationPlease be still, please be patientC-C-C-C-Cause I don’t repeat myself

Listen up we’re halfway through Pay attention know what to doDon’t go stress have some funIt’s only a final, ah where done

To pick up from last timeThe leading strand is doing just fineThe lagging strand 3 to 5Can’t be read can’t go thrive

It needs help in this caseFrom a friend RNA PrimaseThe two RNA create a gapCalled Okazaki Fragments, Oh snap

I need so much help yea, please someone help meYet I feel good bout this test, Oh I guess we’ll seeThis bio thing is real hard, I kinda get itJust in case I wrote this song, extra credit

Remember those gaps from beforeThey are removed they are no moreThis is thanks to a good ligaseAnd don’t forget DNA Polymerase

New double helix is consistedOf old and new chains that are twistedTwo big words, no abbreviationSemi-conservative replication

The last step, not to lateIs to finish, to terminateThen all fixed errors are completeRemember these steps, then repeat

Listen to my explanationGonna give you a educationBetween me and you no stipulationPlease don’t hate cause that good sensationTryin’ to teach you replicationPlease be still, please be patientC-C-C-C-Cause I don’t repeat myself

R Serra, '11

3.5/7.3-4

#1 Basics of Transcription

Be able to name and explain function of each element shown.

#3 Basics of Translation

Every labelled element is required except the names of the three binding sites on the large subunit of the ribosome.

#2 getting into some HL detail...

One BIG difference between prokaryote and eukaryote protein synthesis is the role of intron splicing exclusively in eukaryotes. Read the intro and conclusion carefully and work through all the sections of this animation.

And for those really serious - a research review of transcription by an expert.

21st century graphics...transcription and translation

For reference - Codon Usage Chart - Universally applicable.

Prezi of the combined processes of transcription and translation. Begins with overview and then details of each process.

3.7/8.1

Cellular Respiration

Now we can really start to make some connections - the study of cellular respiration will demonstrate a process that links the importance of (1) the ATP cycle to drive enzymes and active transport across membranes, (2) lysis, synthesis and modification of biomolecules - think breaking down carbon compounds like glucose, pyruvate, formation of new products, (3) how organelles specialize in order to optimize the functional use of particular structures within organelles.

Let's start with the following introduction, courtesy of Crash Course Biology -

Respiration diagrams for annotation...

A thing of beauty...

Animations to break down Electron Transport:

Prep for respiration quiz...answer key to final questions on EB3.7/8.1. Click here.

Prezi for reviewing respiration, introducing photosynthesis

what it's all about?

3.8/8.2

Photosynthesis (Topics 3.8/8.2)

The key here is to take advantage of what you already know about respiration. There are many shared/neatly-contrasting features which connect the two processes. If your understanding of respiration is not yet what you want it to be, studying photosynthesis will be helpful in that respect as well.

Let's start out with a little silliness...

Chlorophyll is a pigment, with a characteristic common to many pigment molecules, alternating C-C double bonds, which make the molecule vulnerable to interaction with light...in the extreme, resulting in "photobleaching." (click on the pictures to enlarge)

Connecting to what was covered in 10th grade chemistry, light energy (here shown as a particle-like photon) interacts with the electrons in a lower energy orbital to excite them into a higher energy state. Chlorophyll molecules in the photosystems I and II become excited and excite the neighboring chlorophyll molecules in turn.

(left) As we saw in our demonstration with "spinach tea," if you illuminate a chlorophyll solution with a high energy UV light, the excess energy is given off as lower energy red fluorescence. (right) The graphs above show the correlation between light absorbed by chlorophyll (colored line) and the amount of photosynthetic activity that occurs of the plants are illuminated with any particular wavelength of light in the visible spectrum.

Now to basic business...light dependent reactions.

Nice, not-to-complicated, but not-too-simple, animation. Think about how the design reflects what is happening in the process. Click on the diagram to start.

And a clear diagram of the Calvin Cycle with "just enough" detail.

Each of these "steps" is truly a series of more complex reactions. The only change to note is that the IB preferred terminology for the product of carboxylation is "G3P" for glycerate-3-phosphate, instead of the term "phosphoglycerate."

How do we know the steps in the light independent reactions? A "lollipop" experiment...

Calvin and his team of scientists used a radioactive atom of carbon. By tracking this special carbon as it travelled through a plant, Calvin could map the process of how plants use carbon and water to create sugar.

Calvin did not use an actual plant. He used a tiny organism called a Chlorella. If you have ever been near the ocean and noticed that the surface of the water looks green, you are probably seeing exactly what Calvin saw-green algae. The single-celled algae was perfect for Calvin's experiment, because the process of photosynthesis is much faster in such a small organism. He filled a glass container with algae, and set up a bright light to enable photosynthesis. Then, Calvin followed the radioactive trail left as the algae made their food.(http://sophia.smith.edu/~dglass/history.html#)

The remaining highlights of the unit include (1) the structure/function relationship between the structure of the chloroplast and the different sets of reactions that occur in each area, (2) the ways to measure photosynthetic rates [keep in mind as we head to a new student-designed lab] and (3) what factors are limiting as one looks at the dependence of photosynthesis rate on light intensity, substrate (carbon dioxide) concentration and temperature (be able to sketch these curves, with labelled axes). Refer to the slide show above for more information on this as needed.

Best check for understanding - can you compare photosynthesis and respiration?
Can you identify useful contrasting features?
Print this image and add your own additional notations.